For example on wikipedia for Switzerland it says the country has an area of 41,285 km². Does this take into account that a lot of that area is actually angled at a steep inclination, thus the actual surface area is in effect larger than what you would expect when looking onto a map in satellite view?
It’s probably aware of them, but generally no. Most slopes for driving on are smooth enough to be pretty negligible unless you’re going hundreds of miles or more, in which case fives of miles won’t make much difference either.
But if you’re traveling by bike those small slopes may make some parts of the ride significantly more difficult or easier, and for cars may impact fuel efficiency in a way much more significant than just counting the extra distance traveled. So many navigation systems will still account for slope, even if they don’t necessarily acknowledge the length of your path as precisely as you may have hoped